The proposed work aims to understand how chromatin diminution, the programmed excision of DNA from the genome of somatic cells, acts as a mechanism of genome defense against transposable elements (TEs). To accomplish this, we will study a biological system in which the host germline and somatic genomes possess dramatic differences in size and architecture, reflecting dramatically different TE loads. Microcrustacean copepods, like most animals, have clearly differentiated germline and somatic genomes; however, some species possess germline genomes that are five to 75 times larger than their somatic genomes. This size difference results from two poorly understood processes operating over very different timescales: (1) large-scale proliferation of transposable elements and other repetitive DNA in the germline genome led to a dramatic increase in germline genome size over evolutionary timescales, and (2) large-scale elimination of these repetitive sequences from the presomatic cell lineage during embryonic development causes massive decreases in somatic genome size over ontogenetic timescales. This genomic downsizing in the soma is called chromatin diminution. Such massive losses of DNA during the lifecycle in copepods facilitates the study of genome reorganization that accompanies germline-soma differentiation. These heritable changes are highly programmed and precise with respect to ontogenetic timing, location of chromosomal breakage, and new telomere formation. We will study these processes in the zooplankton Mesocyclops edax, which has an adult germline genome size five-fold larger than its somatic genome size. Our proposed research has three aims. In Aim 1, we will identify the TEs and other repetitive sequences that are targeted for deletion from the somatic genome during chromatin diminution using genomic sequence and qPCR data. In Aim 2, we will test the hypothesis that the elements targeted for deletion during chromatin diminution are the youngest and most active (and therefore the most potentially deleterious) using transcriptome data and statistical analyses of genomic sequence data. In Aim 3, we will test the hypothesis that the elements targeted for deletion during chromatin diminution are spatially clustered in the genome using FISH. Taken together, these Aims will discover the sequence identities, relative ages and abundances, activity levels, and spatial distributions of the transposable elements that are preferentially excised from the somatic genome, underlying the differences in genome size between germline and soma. This represents an important first step towards our long-term goal of understanding the molecular mechanism and functional significance of this form of TE defense.